They don't want parity - they want money. They want to curb spending on players, which is why they are capping these things. There is some secondary consideration of competitive balance, but that is more for the marketing than anything.
You are right that things can be harder. At the same time, the penalties MLB has put on spending are only somewhat powerful. The surcharges can add up - you'll have to see what ownership will be willing to swallow - but the draft pick penalties are basically zero. (10 draft slots for a good team does not alter the value of the pick much at all)